-package jalview.gui;\r
-\r
-import jalview.jbgui.GFinder;\r
-import jalview.datamodel.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-import java.util.*;\r
-import java.awt.*;\r
-\r
-public class Finder extends GFinder\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- JInternalFrame frame;\r
- SuperGroup searchGroup;\r
-\r
- int seqIndex = 0;\r
- int resIndex = 0;\r
- public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)\r
- {\r
- this.av = av;\r
- this.ap = ap;\r
- frame = f;\r
-\r
- // all a big pain, but we need to wait until the frame is visible before the textfield can\r
- // obtain the focus/////////////////////////\r
- frame.addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameOpened(InternalFrameEvent evt)\r
- {\r
- SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- { textfield.requestFocus(); }\r
- });\r
- }\r
-\r
- public void internalFrameClosing(InternalFrameEvent evt)\r
- {\r
- cancel_actionPerformed(null);\r
- }\r
-});\r
-\r
- }\r
-\r
- public void textfield_actionPerformed(ActionEvent e)\r
- {\r
- doSearch(false);\r
- }\r
-\r
- public void findNext_actionPerformed(ActionEvent e)\r
- {\r
- doSearch(false);\r
- }\r
-\r
- public void findAll_actionPerformed(ActionEvent e)\r
- {\r
- resIndex=0;\r
- seqIndex=0;\r
- doSearch(true);\r
- }\r
-\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( null );\r
- ap.idPanel.highlightSearchResults( null );\r
- // frame.setClosed(true);\r
- }catch(Exception ex){ }\r
- }\r
-\r
-\r
- public void createNewGroup_actionPerformed(ActionEvent e)\r
- {\r
- for(int i=0; i<searchGroup.getSize(); i++)\r
- av.alignment.addGroup( searchGroup.getGroupeAt(i));\r
-\r
- ap.av.alignment.addSuperGroup(searchGroup);\r
- ap.highlightSearchResults( null );\r
- }\r
-\r
-\r
- void doSearch(boolean findAll)\r
- {\r
- createNewGroup.setEnabled(false);\r
-\r
- String searchString = textfield.getText().toUpperCase();\r
-\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
-\r
- ArrayList searchResults = new ArrayList();\r
- int [] allResults = null;\r
-\r
- Sequence seq;\r
- String item=null;\r
- boolean found = false;\r
-\r
- ////// is the searchString a residue number?\r
- try{\r
- int res = Integer.parseInt(searchString);\r
- found = true;\r
-\r
- if(av.getSelectionGroup().getSize()>0)\r
- seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));\r
- else\r
- seq = (Sequence)av.getAlignment().getSequenceAt(0);\r
-\r
- searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );\r
- searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
- searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
-\r
- }catch(NumberFormatException ex){}\r
- ///////////////////////////////////////////////\r
-\r
-\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
- Color [] newColors = new Color[24];\r
- for(int i=0; i<24; i++)\r
- newColors[i] = new Color(60,160,115);\r
-\r
- ucs.setColourScheme(newColors);\r
-\r
- searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
-\r
- int end = av.alignment.getHeight();\r
-\r
- SequenceGroup selection = av.getSelectionGroup();\r
- if(selection!=null)\r
- if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))\r
- selection = null;\r
-\r
- while( !found && seqIndex<end)\r
- {\r
- seq = (Sequence)av.alignment.getSequenceAt(seqIndex);\r
-\r
-\r
- if(selection!=null && !selection.sequences.contains(seq))\r
- {\r
- seqIndex++;\r
- resIndex=0;\r
- continue;\r
- }\r
-\r
- item = seq.getSequence().toUpperCase();\r
-\r
- if(selection!=null && selection.getEndRes()<av.alignment.getWidth())\r
- item = item.substring(0, selection.getEndRes()+1);\r
-\r
- ///Shall we ignore gaps????\r
- StringBuffer noGaps = new StringBuffer();\r
- int insertCount=0;\r
- ArrayList spaces = new ArrayList();\r
-\r
- for (int j=0; j < item.length(); j++)\r
- {\r
-\r
- if(!jalview.util.Comparison.isGap(item.charAt(j)))\r
- {\r
- noGaps.append(item.charAt(j));\r
- spaces.add(new Integer(insertCount));\r
- }\r
- else\r
- insertCount++;\r
- }\r
-\r
-\r
-\r
- for(int r = resIndex; r<noGaps.length(); r++)\r
- {\r
-\r
- if( regex.searchFrom( noGaps.toString(), r ) )\r
- {\r
- resIndex = regex.matchedFrom();\r
- if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())\r
- continue;\r
-\r
- searchResults.add( Integer.toString( seqIndex) );\r
- searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );\r
- searchResults.add( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString()) ) );\r
-\r
- SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
- resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,\r
- regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString())\r
- );\r
- sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));\r
- searchGroup.addGroup( sg );\r
-\r
- if(!findAll)\r
- {\r
- // thats enough, break and display the result\r
- found = true;\r
- resIndex++;\r
- break;\r
- }\r
-\r
- r=resIndex;\r
- }\r
- }\r
- if(!found)\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
- }\r
- }\r
-\r
-\r
- ArrayList idMatch = new ArrayList();\r
- for(int id = 0; id<av.alignment.getHeight(); id++)\r
- {\r
- if( regex.search( av.alignment.getSequenceAt(id).getName() ) )\r
- idMatch.add( av.alignment.getSequenceAt(id) );\r
- }\r
-\r
- if(searchResults.size()==0 && idMatch.size()>0)\r
- ap.idPanel.highlightSearchResults( idMatch );\r
-\r
-\r
- if(searchResults.size()>0)\r
- {\r
- allResults = new int[searchResults.size()];\r
- for(int i=0; i<searchResults.size(); i++)\r
- allResults[i] = Integer.parseInt(searchResults.get(i).toString());\r
-\r
- createNewGroup.setEnabled(true);\r
- }\r
- else\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);\r
- resIndex=0;\r
- seqIndex=0;\r
- }\r
-\r
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( allResults );\r
-\r
- if (findAll)\r
- {\r
- String message = (searchResults.size()/3) + " matches found.";\r
- JOptionPane.showInternalMessageDialog(this, message, null,\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Finder extends GFinder
+{
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ JInternalFrame frame;
+
+ int seqIndex = 0;
+
+ int resIndex = -1;
+
+ SearchResults searchResults;
+
+ /**
+ * Creates a new Finder object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param ap
+ * DOCUMENT ME!
+ * @param f
+ * DOCUMENT ME!
+ */
+ public Finder()
+ {
+ this(null, null);
+ focusfixed = false;
+ }
+
+ public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
+ {
+ av = viewport;
+ ap = alignPanel;
+ focusfixed = true;
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "Find", 340, 110);
+
+ textfield.requestFocus();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void findNext_actionPerformed(ActionEvent e)
+ {
+ if (getFocusedViewport())
+ {
+ doSearch(false);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void findAll_actionPerformed(ActionEvent e)
+ {
+ if (getFocusedViewport())
+ {
+ resIndex = -1;
+ seqIndex = 0;
+ doSearch(true);
+ }
+ }
+
+ /**
+ * do we only search a given alignment view ?
+ */
+ private boolean focusfixed;
+
+ /**
+ * if !focusfixed and not in a desktop environment, checks that av and ap are
+ * valid. Otherwise, gets the topmost alignment window and sets av and ap
+ * accordingly
+ *
+ * @return false if no alignment window was found
+ */
+ boolean getFocusedViewport()
+ {
+ if (focusfixed || Desktop.desktop == null)
+ {
+ if (ap != null && av != null)
+ {
+ return true;
+ }
+ // we aren't in a desktop environment, so give up now.
+ return false;
+ }
+ // now checks further down the window stack to fix bug
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int f = 0; f < frames.length; f++)
+ {
+ JInternalFrame frame = frames[f];
+ if (frame != null && frame instanceof AlignFrame)
+ {
+ av = ((AlignFrame) frame).viewport;
+ ap = ((AlignFrame) frame).alignPanel;
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void createNewGroup_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] seqs = new SequenceI[searchResults.getSize()];
+ SequenceFeature[] features = new SequenceFeature[searchResults
+ .getSize()];
+
+ for (int i = 0; i < searchResults.getSize(); i++)
+ {
+ seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
+
+ features[i] = new SequenceFeature(textfield.getText().trim(),
+ "Search Results", null, searchResults.getResultStart(i),
+ searchResults.getResultEnd(i), "Search Results");
+ }
+
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.showSeqFeatures.setSelected(true);
+ av.setShowSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ }
+
+ /**
+ * incrementally search the alignment
+ *
+ * @param findAll
+ * true means find all results and raise a dialog box
+ */
+ void doSearch(boolean findAll)
+ {
+ createNewGroup.setEnabled(false);
+
+ String searchString = textfield.getText().trim();
+
+ if (searchString.length() < 1)
+ {
+ return;
+ }
+ // TODO: extend finder to match descriptions, features and annotation, and
+ // other stuff
+ // TODO: add switches to control what is searched - sequences, IDS,
+ // descriptions, features
+ jalview.analysis.Finder finder = new jalview.analysis.Finder(
+ av.alignment, av.getSelectionGroup(), seqIndex, resIndex);
+ finder.setCaseSensitive(caseSensitive.isSelected());
+ finder.setFindAll(findAll);
+
+ finder.find(searchString); // returns true if anything was actually found
+
+ seqIndex = finder.getSeqIndex();
+ resIndex = finder.getResIndex();
+
+ searchResults = finder.getSearchResults(); // find(regex,
+ // caseSensitive.isSelected(), )
+ Vector idMatch = finder.getIdMatch();
+ boolean haveResults = false;
+ // set or reset the GUI
+ if ((idMatch.size() > 0))
+ {
+ haveResults = true;
+ ap.idPanel.highlightSearchResults(idMatch);
+ }
+ else
+ {
+ ap.idPanel.highlightSearchResults(null);
+ }
+
+ if (searchResults.getSize() > 0)
+ {
+ haveResults = true;
+ createNewGroup.setEnabled(true);
+ }
+ else
+ {
+ searchResults = null;
+ }
+
+ // if allResults is null, this effectively switches displaySearch flag in
+ // seqCanvas
+ ap.highlightSearchResults(searchResults);
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+ // 'SelectRegion' selection
+ if (!haveResults)
+ {
+ JOptionPane.showInternalMessageDialog(this, "Finished searching",
+ null, JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
+ }
+
+ if (findAll)
+ {
+ String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ : "";
+ if (searchResults != null)
+ {
+ if (idMatch.size() > 0 && searchResults.getSize() > 0)
+ {
+ message += " and ";
+ }
+ message += searchResults.getSize() + " subsequence matches found.";
+ }
+ JOptionPane.showInternalMessageDialog(this, message, null,
+ JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
+ }
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff